Shift iter counter to use 0 at initial time

The addition of an analysis call on the initial data resulted
in the Nth time step to correspond with iteration N+1. This isn't
a problem, just dissatisfying.

src/BaseCase.cpp

@@ -413,7 +413,7 @@ void BaseCase::write_diagnostics(string header, string line,
     FILE * diagnos_file = fopen("diagnostics.txt","a");
     assert(diagnos_file);
     // print header
-    if (iter == 1 and !restarting) {
+    if (iter == 0 and !restarting) {
         fprintf(diagnos_file,"%s\n",clean_header.c_str());
     }
     // print the line of values
@@ -487,7 +487,7 @@ void BaseCase::stresses_top(TArrayn::DTArray & u, TArrayn::DTArray & v, TArrayn:
     if (master()) {
         FILE * stresses_file = fopen("stresses_top.txt","a");
         assert(stresses_file);
-        if ( itercount==1 and !restarting )
+        if ( itercount==0 and !restarting )
             fprintf(stresses_file,"Time, "
                     "Top_tx_tot, Top_tx_abs, Top_ty_tot, Top_ty_abs, Top_ts\n");
         fprintf(stresses_file,"%.17f, "
@@ -533,7 +533,7 @@ void BaseCase::stresses_bottom(TArrayn::DTArray & u, TArrayn::DTArray & v, TArra
     if (master()) {
         FILE * stresses_file = fopen("stresses_bottom.txt","a");
         assert(stresses_file);
-        if ( itercount==1 and !restarting )
+        if ( itercount==0 and !restarting )
             fprintf(stresses_file,"Time, "
                     "Bottom_tx_tot, Bottom_tx_abs, Bottom_ty_tot, Bottom_ty_abs, Bottom_ts\n");
         fprintf(stresses_file,"%.17f, "

src/NSIntegrator_impl.cc

@@ -35,6 +35,9 @@ namespace NSIntegrator {
          /* Control framework for a full run.  At the first timestep(s), take
             fractional timesteps to start up. */
       
+          // Analyze the initial conditions
+          usercode->analysis(times[0],us[0],vs[0],ws[0],tracers_now,pressure);
+
          while (times[0] < (fintime - 1e-8*fabs(fintime))) {
             // Since we're not done, we need to take a timestep.
 
@@ -84,9 +87,6 @@ namespace NSIntegrator {
                   total time integration error.  So, if we're starting up,
                   we take a small timestep and progressively double it. */
                if (times[-1] == times[-2]) {
-                  // Analyze the initial conditions
-                  usercode->analysis(times[0],us[0],vs[0],ws[0],tracers_now,pressure);
-
                   /* Startup, so take a tiny timestep */
                   my_step = the_timestep/64;
                   starting_step = true;

src/Science.cpp

@@ -335,7 +335,7 @@ void compute_Background_PE(double & BPE_tot, TArrayn::DTArray & rho,
     static vector < pair<double, double> > height_width(Nx);
 
     // Stuff to do once at the beginning
-    if (iter == 1) {
+    if (iter == 0) {
         // create array of voxels
         quad3 = alloc_array(Nx,Ny,Nz);
         *quad3 = (*get_quad_x())(ii)*(*get_quad_y())(jj)*(*get_quad_z())(kk);

src/cases/gravity_current/gravity_current.cpp

@@ -188,10 +188,8 @@ class userControl : public BaseCase {
         /* Basic analysis: compute secondary variables, and save fields and diagnostics */
         void analysis(double time, DTArray & u, DTArray & v, DTArray & w,
                 vector<DTArray *> & tracers, DTArray & pressure) {
-            // increase counter
-            iter++;
             // Set-up
-            if ( iter == 1 ) {
+            if ( iter == 0 ) {
                 if ( compute_enstrophy or compute_dissipation or
                         compute_stresses_top or compute_stresses_bottom ) {
                     temp1 = alloc_array(Nx,Ny,Nz);
@@ -388,6 +386,8 @@ class userControl : public BaseCase {
                     plot_number, u, v, w, tracers);
             // Change dump log file if successfully reached final time
             successful_dump(plot_number, final_time, plot_interval);
+            // increase counter
+            iter++;
         }
 
         // User specified variables to dump